In my current system I have a velodyne 1215x hooked up to the sub pre-out of my Denon AVR-3600,it works great. My front mains are Polk ls70's,center is a Polk cs350-ls,surrounds are Polk ls f/x's.Ampifier is an Adcom gfa-7000. I just bought a Velodyne dls-4000r and wonder how I should integrate it into the system? Should I use the new sub to handle the lfe channel and the 1215x to to handle the bass for the mains or vice versa?

The Y adaptor will allow both subs to run off the LFE channel, it can be complicated t adjust two subs on the same line (I've done it with four this way) the best advice I have is to first do each sub separately, find where they sound best in the room, calibrate them, then move onto the next sub. Turn one off at a time, working on the other then turn the other off and work on the last one. Trying to tune them in both at the same time is highly NOT recommended as you'll go insane before you get it right!

So I am supposed to plug a Y coupler into the mono LFE rca plug on the back of my pre-amp,then run a line to each subwoofer off of that? The subwoofers each have stereo rca plugs, so do I have to put another Y coupler on the mono rca line going to the sub so that it can plug into the sub's stereo plugs? Will splitting the signal that many times create any problems?

Most subs accept a mono input on one or either channel (if one it's usually the 'left' channel) You can split it where ever is convenient, either at the pre/pro LFE out or at one of the subs if it is easier.